Shanye, you have had a great win here, with a lot of help from MEL_traveller. I can't believe your attitude, at worst it is xenophobic with regard to travelling through Egypt, if I was doing what you are doing I would be disappointed I wasn't allowed to have a couple of days stopover to go exploring! "Australian looking", what does that even mean? Are you white, black, brown? Speak English, French, Thai, Japanese? It doesn't even matter, your just another person.
Also the argument you are now pitching about it being an indirect flight doesn't stack up with the rest of your itinerary you have as it is all over the place! To get 4 seats in J (let alone in Y) at such short notice on what looks like a great product is a win all round. Right now I would accept what you have and what a great deal you have got and go ahead and enjoy your trip. Stressing yourself out by just trying to make it 'better' is ridiculous.
Also, ever heard the saying that "if you can't afford travel insurance you can't afford to travel"?